Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II)^1,2,3,4,5. Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5′-to-3′ exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5′ terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.

强大的基因转录需要有效的终止。真核生物利用保守的核糖核酸外切酶介导的机制来终止 RNA 聚合酶 II (Pol II) 的 mRNA 转录^1,2,3,4,5。在这里，我们报道了与 5'-to-3' 核糖核酸外切酶 Rat1 及其伴侣 Rai1 结合的酿酒酵母Pol II 终止前转录复合物的两种低温电子显微镜结构。我们的结构表明 Rat1 取代了延伸因子 Spt5 以停靠在 Pol II 茎结构域上。 Rat1 屏蔽 Pol II 的 RNA 出口通道，引导新生 RNA 走向其活性中心，并在新生 RNA 的 5' 末端堆叠三个核苷酸。这些结构进一步表明 Rat1 在缩短 RNA 时会向 Pol II 方向旋转。我们的结果提供了酵母中 Rat1 介导的 Pol II mRNA 转录终止和其他真核生物中核糖核酸外切酶介导的 mRNA 转录终止的结构机制。